Fix bug where 0 patients was assumed all patients in genomic processing

hms-dbmi · Jan 26, 2024 · 22129ae · 22129ae
1 parent e93f9f7
commit 22129ae
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java b/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java
@@ -130,7 +130,7 @@ protected Set<Integer> applyBooleanLogic(List<Set<Integer>> filteredIdSets) {
 	protected Set<Integer> idSetsForEachFilter(Query query) {
 		DistributableQuery distributableQuery = getDistributableQuery(query);
 
-		if (distributableQuery.hasFilters()) {
+		if (!distributableQuery.getPatientIds().isEmpty() && distributableQuery.hasFilters()) {
             Mono<BigInteger> patientMaskForVariantInfoFilters = genomicProcessor.getPatientMask(distributableQuery);
 			return patientMaskForVariantInfoFilters.map(genomicProcessor::patientMaskToPatientIdSet).block();
         }
@@ -156,7 +156,7 @@ private DistributableQuery getDistributableQuery(Query query) {
 
 		Set<Integer> phenotypicPatientSet;
 		//AND logic to make sure all patients match each filter
-		if(patientIdSets.size()>0) {
+		if(!patientIdSets.isEmpty()) {
 			phenotypicPatientSet = applyBooleanLogic(patientIdSets);
 		} else {
             // if there are no patient filters, use all patients.

diff --git a/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandler.java b/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandler.java
@@ -33,9 +33,8 @@ public BigInteger getPatientIdsForIntersectionOfVariantSets(Set<Integer> patient
             Set<Integer> patientIds = Arrays.asList(
                     variantService.getPatientIds()).stream().map((String id)->{
                 return Integer.parseInt(id);}).collect(Collectors.toSet());
-            if(!patientSubset.isEmpty()) {
-                // for now, empty means there were no phenotypic filters and all patients are eligible. we should
-                // change this to be nullable or have a separate method, this is very counter intuitive
+            if(patientSubset == null) {
+                // for now, null means there were no phenotypic filters and all patients are eligible
                 patientsInScope = Sets.intersection(patientIds, patientSubset);
             } else {
                 patientsInScope = patientIds;